Iodine in PDB 5iqy: Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method

All present enzymatic activity of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method:
1.8.5.1;

The structure of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method, PDB code: 5iqy was solved by B.K.Das, A.Kumar, P.Manidola, A.Arockiasamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.78 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.890, 132.080, 97.570, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iodine atom in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method (pdb code 5iqy). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 26 binding sites of Iodine where determined in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method, PDB code: 5iqy:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:53.8 occ:1.00 O A:HOH430 3.4 48.3 1.0 O A:ALA130 3.7 51.6 1.0 N A:GLY100 3.7 45.0 1.0 C A:ALA130 4.0 49.4 1.0 CA A:VAL99 4.1 51.8 1.0 CA A:LEU131 4.1 38.2 1.0 N A:LEU131 4.2 41.4 1.0 CG1 A:VAL99 4.3 55.8 1.0 CB A:ALA130 4.4 48.5 1.0 C A:VAL99 4.4 49.6 1.0 CB A:HIS134 4.5 49.3 1.0 CA A:GLY100 4.5 43.4 1.0 CB A:VAL99 4.6 56.3 1.0 CG2 A:VAL99 4.7 59.5 1.0 CB A:LEU131 4.8 33.8 1.0 CA A:ALA130 4.9 49.0 1.0

Iodine binding site 2 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:56.1 occ:0.86 N A:ALA150 3.8 25.3 1.0 CB A:ALA149 3.9 24.5 1.0 CA A:ALA150 4.0 25.0 1.0 CB A:ALA150 4.2 28.4 1.0 O A:HOH480 4.2 34.9 1.0 C A:ALA149 4.3 26.8 1.0 OG1 A:THR92 4.3 39.7 1.0 NH2 A:ARG25 4.3 24.6 1.0 CB A:THR92 4.4 41.0 1.0 O A:HOH455 4.7 51.7 1.0 CA A:ALA149 4.7 23.0 1.0 O A:ALA149 4.8 25.2 1.0 O A:HOH403 4.9 24.8 1.0

Iodine binding site 3 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:50.6 occ:0.76 N A:ASP15 3.7 40.6 1.0 OD2 A:ASP15 3.7 74.7 1.0 CB A:ASP15 3.8 46.5 1.0 CA A:ALA13 3.8 39.5 1.0 C A:ALA13 3.9 42.3 1.0 N A:PRO14 4.0 40.9 1.0 CG A:ASP15 4.0 63.1 1.0 CD A:PRO14 4.0 45.1 1.0 CB A:ALA13 4.2 39.0 1.0 CA A:ASP15 4.2 40.7 1.0 O A:ALA13 4.6 41.1 1.0 CG1 A:ILE16 4.6 36.4 1.0 C A:ASP15 4.7 39.8 1.0 C A:PRO14 4.7 43.9 1.0 CD1 A:ILE16 4.8 51.2 1.0 N A:ILE16 4.9 32.2 1.0 CA A:PRO14 4.9 39.9 1.0

Iodine binding site 4 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:49.5 occ:0.66 O A:HOH470 3.5 34.2 1.0 CZ A:PHE104 3.7 24.4 1.0 CD A:PRO21 3.9 14.0 1.0 CG A:PRO21 4.0 18.3 1.0 CE2 A:PHE104 4.1 26.3 1.0 CE2 A:PHE22 4.1 21.8 1.0 CZ2 A:TRP207 4.3 27.0 1.0 CH2 A:TRP207 4.3 28.0 1.0 NZ A:LYS210 4.8 71.5 1.0 CE1 A:PHE104 4.9 25.7 1.0 CD2 A:PHE22 4.9 18.3 1.0 CZ A:PHE22 4.9 19.7 1.0 O A:HOH404 4.9 29.1 1.0

Iodine binding site 5 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:46.5 occ:0.62 OG A:SER153 3.5 24.8 1.0 NZ A:LYS157 3.5 37.2 1.0 CD A:LYS157 3.8 22.0 1.0 O A:HOH413 3.9 37.0 1.0 N A:LEU154 4.0 22.3 1.0 CA A:LEU154 4.0 22.7 1.0 CE A:LYS157 4.1 33.5 1.0 O A:HOH455 4.1 51.7 1.0 CB A:LEU154 4.2 24.9 1.0 CA A:SER101 4.2 43.4 1.0 C A:SER153 4.2 24.0 1.0 CB A:SER153 4.2 20.0 1.0 CD1 A:LEU154 4.3 29.2 1.0 O A:HOH489 4.3 28.6 1.0 O A:SER153 4.4 22.6 1.0 N A:SER101 4.5 44.5 1.0 O A:GLY100 4.6 43.6 1.0 O A:VAL99 4.6 46.5 1.0 O A:HOH438 4.6 28.0 1.0 C A:GLY100 4.7 45.9 1.0 CB A:SER101 4.7 46.7 1.0 CG A:LEU154 4.8 29.8 1.0 CA A:SER153 4.9 18.6 1.0 O A:ALA150 5.0 26.5 1.0

Iodine binding site 6 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:59.5 occ:0.62 CG A:PRO94 3.8 72.8 1.0 I A:IOD321 3.8 51.1 0.3 CB A:PRO94 4.3 65.3 1.0 N A:GLU95 4.5 69.3 1.0 CB A:GLU95 4.8 76.1 1.0 CD A:PRO94 4.9 66.0 1.0 CA A:GLU95 5.0 70.9 1.0

Iodine binding site 7 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:54.9 occ:0.65 CG2 A:VAL108 3.8 24.8 1.0 CA A:PRO105 3.9 28.5 1.0 CB A:VAL108 4.0 27.9 1.0 CG1 A:VAL108 4.1 28.0 1.0 CE2 A:PHE104 4.2 26.3 1.0 CD2 A:PHE104 4.2 24.6 1.0 CB A:PRO105 4.2 31.0 1.0 N A:PRO105 4.5 27.4 1.0 O A:PHE104 4.9 29.3 1.0 C A:PHE104 5.0 30.1 1.0 O A:PRO105 5.0 33.8 1.0

Iodine binding site 8 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:54.9 occ:0.60 O A:HOH447 3.3 32.2 1.0 N A:SER45 3.7 39.6 1.0 CB A:LEU44 3.9 32.9 1.0 CG2 A:VAL11 4.1 30.3 1.0 CB A:SER45 4.1 44.0 1.0 C A:LEU44 4.2 41.5 1.0 O A:HOH459 4.2 33.0 1.0 CA A:LEU44 4.3 34.7 1.0 N A:LEU44 4.3 34.0 1.0 CA A:SER45 4.4 41.1 1.0 CE A:LYS8 4.4 35.6 1.0 O A:HOH444 4.7 31.4 1.0 OG A:SER45 4.8 52.2 1.0 OD1 A:ASP43 4.8 36.9 1.0 CG A:LEU44 4.8 36.0 1.0 O A:HOH428 5.0 31.5 1.0

Iodine binding site 9 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I309 b:45.1 occ:0.63 O A:HOH448 3.6 54.2 1.0 CB A:ALA72 3.9 25.8 1.0 O A:HOH446 3.9 41.1 1.0 OE1 A:GLU57 4.0 44.4 1.0 CG A:LYS59 4.0 60.3 1.0 CD A:GLU57 4.1 57.1 1.0 CB A:LYS59 4.1 37.0 1.0 CB A:GLU57 4.1 30.9 1.0 CG A:GLU57 4.4 39.1 1.0 OE2 A:GLU57 4.5 53.6 1.0

Iodine binding site 10 out of 26 in the Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Apo-Dehydroascorbate Reductase From Pennisetum Glaucum Phased By Iodide-Sad Method within 5.0Å range: probe atom residue distance (Å) B Occ A:I310 b:57.6 occ:0.53 CE A:LYS40 3.7 58.0 1.0 CE3 A:TRP50 3.8 46.6 1.0 NZ A:LYS40 4.2 67.1 1.0 CB A:TRP50 4.4 52.7 1.0 CD2 A:TRP50 4.5 47.3 1.0 CD1 A:ILE54 4.5 54.0 1.0 CZ3 A:TRP50 4.5 45.4 1.0 CD A:LYS40 4.5 51.2 1.0 CG A:TRP50 4.8 51.1 1.0 O A:TRP50 4.9 50.8 1.0 CZ2 A:TRP70 4.9 50.3 1.0

B.K.Das, A.Kumar, P.Maindola, S.Mahanty, S.K.Jain, M.K.Reddy, A.Arockiasamy. Non-Native Ligands Define the Active Site of Pennisetum Glaucum (L.) R. Br Dehydroascorbate Reductase Biochem.Biophys.Res.Commun. V. 473 1152 2016.
ISSN: ESSN 1090-2104
PubMed: 27067046
DOI: 10.1016/J.BBRC.2016.04.031